📦 genometools

G

• gt(1)The GenomeTools genome analysis system.✨
• gt-bed_to_gff3(1)Parse BED file and convert it to GFF3.✨
• gt-cds(1)Add CDS (coding sequence) features to exon features given in GFF3 file.✨
• gt-chain2dim(1)Chain pairwise matches.✨
• gt-chseqids(1)Change sequence ids by the mapping given in a mapping file.✨
• gt-clean(1)Remove all files in the current directory which are automatically created by gt.✨
• gt-compreads(1)Call a fastq file compression tool.✨
• gt-compreads-compress(1)Generates compact encoding for fastq data.✨
• gt-compreads-decompress(1)Decodes a file of compressed reads.✨
• gt-compreads-refcompress(1)Generates compact encoding for fastq data using Reference Compressed Reads (RCR).✨
• gt-compreads-refdecompress(1)Decodes a given RCR (Reference Compressed Reads).✨
• gt-condenseq(1)Call one of the CONDENSER tools to prepare or manipulate redundancy compressed genomic data.✨
• gt-congruence(1)Call a congruence subtool and pass argument(s) to it.✨
• gt-congruence-spacedseed(1)Match spaced seeds.✨
• gt-convertseq(1)Parse and convert sequence file formats (FASTA/FASTQ, GenBank, EMBL).✨
• gt-csa(1)Transform spliced alignments from GFF3 file into consensus spliced alignments.✨
• gt-dot(1)Prints feature graphs in dotfile format.✨
• gt-dupfeat(1)Duplicate internal feature nodes in given GFF3 files.✨
• gt-encseq(1)Call an encoded sequence manipulation tool and pass argument(s) to it.✨
• gt-encseq-bench(1)Perform benchmark on extractions from encseq.✨
• gt-encseq-bitextract(1)Extracts internal data from encoded sequences.✨
• gt-encseq-check(1)Check the consistency of an encoded sequence file.✨
• gt-encseq-decode(1)Decode/extract encoded sequences.✨
• gt-encseq-encode(1)Encode sequence files (FASTA/FASTQ, GenBank, EMBL) efficiently.✨
• gt-encseq-info(1)Display meta-information about an encoded sequence.✨
• gt-encseq-md5(1)Display MD5 sums for an encoded sequence.✨
• gt-encseq-sample(1)Decode/extract encoded sequences by random choice.✨
• gt-encseq2spm(1)Compute suffix prefix matches from encoded sequence.✨
• gt-eval(1)Compare annotation files and show accuracy measures (prediction vs. reference).✨
• gt-extractfeat(1)Extract features given in GFF3 file from sequence file.✨
• gt-extractseq(1)Extract sequences from given sequence file(s) or fastaindex.✨
• gt-fastq_sample(1)Print samples by random choice from given FASTQ files using at least n sequence-chars. Output is fastq/fasta format depending on whether qualities are available.✨
• gt-featureindex(1)Retrieve annotations from a persistent feature index as GFF3 output.✨
• gt-fingerprint(1)Compute MD5 fingerprints for each sequence given in a set of sequence files.✨
• gt-genomediff(1)Calculates Kr: pairwise distances between genomes.✨
• gt-gff3(1)Parse, possibly transform, and output GFF3 files.✨
• gt-gff3_to_gtf(1)Parse GFF3 file(s) and show them as GTF2.2.✨
• gt-gff3validator(1)Strictly validate given GFF3 files.✨
• gt-gtf_to_gff3(1)Parse GTF2.2 file and convert it to GFF3.✨
• gt-hop(1)Cognate sequence-based homopolymer error correction.✨
• gt-id_to_md5(1)Change sequence IDs in given GFF3 files to MD5 fingerprints of the corresponding sequences.✨
• gt-inlineseq_add(1)Adds inline sequences from external source to GFF3 input.✨
• gt-inlineseq_split(1)Split GFF3 annotations with inline sequences into separate files.✨
• gt-interfeat(1)Add intermediary features between outside features in given GFF3 file(s).✨
• gt-loccheck(1)Checks parent-child containment in GFF3 input.✨
• gt-ltrclustering(1)Cluster features of LTRs.✨
• gt-ltrdigest(1)Identifies and annotates sequence features in LTR retrotransposon candidates.✨
• gt-ltrharvest(1)Predict LTR retrotransposons.✨
• gt-matchtool(1)Parse match formats and/or invoke matching tools.✨
• gt-matstat(1)Compute matching statistics.✨
• gt-md5_to_id(1)Change MD5 fingerprints used as sequence IDs in given GFF3 files to ``regular'' ones.✨
• gt-merge(1)Merge sorted GFF3 files in sorted fashion.✨
• gt-mergefeat(1)Merge adjacent features without children of the same type in given GFF3 file(s).✨
• gt-mkfeatureindex(1)Creates a new FeatureIndex from annotation data.✨
• gt-mmapandread(1)Map the supplied files into memory and read them once.✨
• gt-orffinder(1)Identifies ORFs (open reading frames) in sequences.✨
• gt-packedindex(1)Call apacked index subtool and pass argument(s) to it.✨
• gt-prebwt(1)Precompute bwt-bounds for some prefix length.✨
• gt-readjoiner(1)Readjoiner: a string graph-based sequence assembler.✨
• gt-readjoiner-assembly(1)Construct string graph and output contigs.✨
• gt-readjoiner-overlap(1)Compute suffix prefix matches from encoded sequence.✨
• gt-readjoiner-prefilter(1)Remove contained and low-quality reads and encode read set in GtEncseq format.✨
• gt-repfind(1)Compute maximal exact matches (and more).✨
• gt-scriptfilter(1)Get info about and validate Lua script filters.✨
• gt-seed_extend(1)Calculate local alignments using the seed and extend algorithm.✨
• gt-select(1)Select certain features (specified by the used options) from given GFF3 file(s).✨
• gt-seq(1)Parse the given sequence file(s) and construct the corresponding index files.✨
• gt-seqfilter(1)Filter the given sequence file(s) and show the results on stdout.✨
• gt-seqids(1)Show sequence IDs from annotation file.✨
• gt-seqmutate(1)Mutate the sequences of the given sequence file(s).✨
• gt-seqorder(1)Output sequences as MultiFasta in specified order.✨
• gt-seqstat(1)Calculate statistics for fasta file(s).✨
• gt-seqtransform(1)Perform simple transformations on the given sequence file(s).✨
• gt-seqtranslate(1)Translates a nucleotide sequence into a protein sequence.✨
• gt-sequniq(1)Filter out repeated sequences in given sequence files.✨
• gt-shredder(1)Shredder sequence file(s) into consecutive pieces of random length.✨
• gt-shulengthdist(1)Compute distribution of pairwise shustring lengths.✨
• gt-simreads(1)Simulate sequencing reads from random positions in the input sequence(s).✨
• gt-sketch(1)Create graphical representation of GFF3 annotation files.✨
• gt-sketch_page(1)Draw a multi-page PDF/PS representation of an annotation file.✨
• gt-snpper(1)Annotates SNPs according to their effect on the genome as given by a genomic annotation.✨
• gt-speck(1)Checks spec definition compliance in GFF3 input.✨
• gt-splicesiteinfo(1)Show information about splice sites given in GFF3 files.✨
• gt-splitfasta(1)Split the supplied fasta file.✨
• gt-stat(1)Show statistics about features contained in GFF3 files.✨
• gt-tagerator(1)Map short sequence tags in given index.✨
• gt-tallymer(1)Call a tallymer subtool and pass argument(s) to it.✨
• gt-tallymer-mkindex(1)Count and index k-mers in the given enhanced suffix array for a fixed value of k.✨
• gt-tallymer-occratio(1)Compute occurrence ratio for a set of sequences represented by an enhanced suffix array.✨
• gt-tallymer-search(1)Search a set of k-mers in an index constructed by ``gt tallymer mkindex''.✨
• gt-tirvish(1)Identify Terminal Inverted Repeat (TIR) elements,such as DNA transposons.✨
• gt-uniq(1)Filter out repeated feature node graphs in a sorted GFF3 file.✨
• gt-uniquesub(1)Compute length of minimum unique prefixes.✨
• gt-wtree(1)Call an wtree manipulation tool and pass argument(s) to it.✨